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Yorodumi- EMDB-13593: Structure of thermostabilised human NTCP in complex with nanobody 87 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13593 | |||||||||
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Title | Structure of thermostabilised human NTCP in complex with nanobody 87 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information bile acid:sodium symporter activity / regulation of bile acid secretion / bile acid signaling pathway / bile acid and bile salt transport / Recycling of bile acids and salts / response to nutrient levels / response to organic cyclic compound / response to estrogen / cellular response to xenobiotic stimulus / virus receptor activity ...bile acid:sodium symporter activity / regulation of bile acid secretion / bile acid signaling pathway / bile acid and bile salt transport / Recycling of bile acids and salts / response to nutrient levels / response to organic cyclic compound / response to estrogen / cellular response to xenobiotic stimulus / virus receptor activity / basolateral plasma membrane / response to ethanol / plasma membrane Similarity search - Function | |||||||||
Biological species | Lama glama (llama) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Goutam K / Reyes N | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Nature / Year: 2022 Title: Structural basis of sodium-dependent bile salt uptake into the liver. Authors: Kapil Goutam / Francesco S Ielasi / Els Pardon / Jan Steyaert / Nicolas Reyes / Abstract: The liver takes up bile salts from blood to generate bile, enabling absorption of lipophilic nutrients and excretion of metabolites and drugs. Human Na-taurocholate co-transporting polypeptide (NTCP) ...The liver takes up bile salts from blood to generate bile, enabling absorption of lipophilic nutrients and excretion of metabolites and drugs. Human Na-taurocholate co-transporting polypeptide (NTCP) is the main bile salt uptake system in liver. NTCP is also the cellular entry receptor of human hepatitis B and D viruses (HBV/HDV), and has emerged as an important target for antiviral drugs. However, the molecular mechanisms underlying NTCP transport and viral receptor functions remain incompletely understood. Here we present cryo-electron microscopy structures of human NTCP in complexes with nanobodies, revealing key conformations of its transport cycle. NTCP undergoes a conformational transition opening a wide transmembrane pore that serves as the transport pathway for bile salts, and exposes key determinant residues for HBV/HDV binding to the outside of the cell. A nanobody that stabilizes pore closure and inward-facing states impairs recognition of the HBV/HDV receptor-binding domain preS1, demonstrating binding selectivity of the viruses for open-to-outside over inward-facing conformations of the NTCP transport cycle. These results provide molecular insights into NTCP 'gated-pore' transport and HBV/HDV receptor recognition mechanisms, and are expected to help with development of liver disease therapies targeting NTCP. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13593.map.gz | 107.3 MB | EMDB map data format | |
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Header (meta data) | emd-13593-v30.xml emd-13593.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | emd_13593.png | 79.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13593 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13593 | HTTPS FTP |
-Validation report
Summary document | emd_13593_validation.pdf.gz | 393.6 KB | Display | EMDB validaton report |
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Full document | emd_13593_full_validation.pdf.gz | 393.2 KB | Display | |
Data in XML | emd_13593_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_13593_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13593 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13593 | HTTPS FTP |
-Related structure data
Related structure data | 7pqgMC 7pqqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13593.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.008 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Human NTCP in complex with nanobody 87
Entire | Name: Human NTCP in complex with nanobody 87 |
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Components |
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-Supramolecule #1: Human NTCP in complex with nanobody 87
Supramolecule | Name: Human NTCP in complex with nanobody 87 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Lama glama (llama) |
-Macromolecule #1: Nanobody 87
Macromolecule | Name: Nanobody 87 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) / Strain: Lama glama |
Molecular weight | Theoretical: 14.988481 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: QVQLVESGGG LVQAGGSLRL SCAVSGRTTA NYNMGWFRQA PGKEREFVAG IKWSSGSTYV ADSAKGRFTI SRDNAKNSVY LQMDSLKPE DTALYYCAAN YYGVSWFLIS PSSYDYWGQG TQVTVSSHHH HHHEPEA |
-Macromolecule #2: Sodium/bile acid cotransporter
Macromolecule | Name: Sodium/bile acid cotransporter / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 36.652391 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAHTASAPFT FTLPPNFGKR PTDLALSVIL VVMLFIIMLS LGCTMEFSKI KAHLWKPKGL AIALVAQYGI MPLTAFVLGK VFRLNNIEA LAILICGCSP GGNLSNIFSL AMKGDMNLSI VMTTCSTFLA LGMMPLLLYI YSRGIYDGDL KDKVPYKGIV I SLVLVLIP ...String: MAHTASAPFT FTLPPNFGKR PTDLALSVIL VVMLFIIMLS LGCTMEFSKI KAHLWKPKGL AIALVAQYGI MPLTAFVLGK VFRLNNIEA LAILICGCSP GGNLSNIFSL AMKGDMNLSI VMTTCSTFLA LGMMPLLLYI YSRGIYDGDL KDKVPYKGIV I SLVLVLIP CTIGIVLKSK RPQYMRYVIK GGMIIILLCS VAVTVLSAIN VGKSIMFAMT PHLIATSSLM PFIGFLLGYV LS ALFCLNG RCRRTVSMET GCQNVQLCST ILNVAFPPEV IGPLFFFPLL YMIFQLGEGL LLIAIFWCYE KFKTPKDKTK MIY TAATTE ELEVLFQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER Details: The initial model for Nanobody was created using I-TASSER server. Transporter was modelled using NTCP-Nb91 high-resolution structure as the initial model. |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61053 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |